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Dr Alex Bateman

Abstract:

Elucidating novel biochemical pathways in multi-omics data    Metagenomic analyses have emerged as a powerful strategy to identify biomass-degrading enzymes, essential in the production of biofuels.  Standard metagenomic analysis focusses on processing the DNA sequence to reveal the species and proteins within the sample.  This project expand routine analysis to include pathway reconstruction, based on pathways found in Reactome or KEGG.   For example the gut microbiome of certain termites possesses the potential to degrade biomass components, such as arabinoxylans and arabinans [1]. Creating a pipeline to routinely identify novel metabolic capacities has important implications for biotechnology.  As well as pathway reconstruction we will also identify the source organisms of the enzymes in the pathway.     The process of biorefinery requires the breakdown of complex organic materials to hydrocarbons such as ethanol.  Recently, multi-omics datasets have started to be produced [2].  Understanding the metabolome alongside the proteome will be essential for understanding how sophisticated natural biomass-degrading strategies work.   Having tools to combine functional pathway data and metabolomics data may make it possible to understand the entire degradation pathway. Furthermore, it may facilitate the discovery of new pathways, where components of a degradation pathway are absent or where metabolites do not conform. Such tools may also enable, cheaper, function-driven multiomics, whereby only key enzymes or metabolites would be assayed [3].     This project is based at the EMBL-EBI where the student will have access to the data resources and expertise of a wide range of relevant databases such as the EBI Metagenomics Portal, MetaboLights and Reactome.

References:

  1. Bastien G, Arnal G, Bozonnet S, Laguerre S, Ferreira F, Fauré R, Henrissat B,  Lefèvre F, Robe P, Bouchez O, Noirot C, Dumon C, O'Donohue M. Mining for hemicellulases in the fungus-growing termite Pseudacanthotermes militaris using functional metagenomics. Biotechnol Biofuels. 2013;6:78. doi: 10.1186/1754-6834-6-78. PubMed PMID: 23672637.     
  2. Di Girolamo F, Lante I, Muraca M, Putignani L. The Role of Mass Spectrometry in the "Omics" Era. Curr Org Chem. 2013:2891-2905. PubMed PMID: 24376367.
  3. Tasse L, Bercovici J, Pizzut-Serin S, Robe P, Tap J, Klopp C, Cantarel BL, Coutinho PM, Henrissat B, Leclerc M, Doré J, Monsan P, Remaud-Simeon M, Potocki-Veronese G. Functional metagenomics to mine the human gut microbiome for  dietary fiber catabolic enzymes. Genome Res. 2010;20:1605-1612. doi: 10.1101/gr.108332.110. PubMed PMID: 20841432.

Dr Alex Bateman

Dr Alex Bateman
European Bioinformatics Institute
Email:
Office Phone: 01223 494100

Second supervisor:

 Gos Micklem